Peel Holdings, owner of the Manchester Ship Canal and former owner of the Trafford Centre in Manchester, wants to develop a swath of disused dockland containing a multitude of historic buildings as part of its multibillion-pound Liverpool Waters scheme. It features thousands of flats and hundreds of offices, hotels and bars, as well as the 55-storey Shanghai Tower and other skyscrapers.

The scheme envisages two clusters of tall buildings, one near the city centre and a second further north.

But English Heritage has written to Liverpool city council expressing its concerns that a secondary cluster of tall buildings at Clarence Dock will introduce a large and strong vertical form that will "overwhelm the historic, horizontal character of the docklands generally".

The density of development, the mass and scale of the waterfront blocks and the height and scale of the tall buildings "will divorce, rather than connect, the two main parts of the Stanley Dock character area of the world heritage site", English Heritage argues. It believes the development will prevent an appreciation of the relationship between the docks and river that is essential to an understanding of the site.

Furthermore, it says the development will detract from the historical primacy of the Pier Head buildings and will harm the setting of the Stanley Dock warehouses by largely obscuring them.

It adds: "The scale of the development will compromise and unbalance the historic urban landscape of Liverpool as a whole." The heritage organisation also points out that there is a lack of clarity in what the Shanghai Tower development will involve, as there are contradictions within Peel Holdings' plans.

Henry Owen-John, planning director, north-west, for English Heritage said: "One of the things that we're anxious to make clear is that while we have serious problems with the effect on the world heritage status these proposals will have, we're also aware of the significant benefits delivered, particularly a programme that would drive jobs and growth …

"We're not actually specifically asking for the application to be called in [to the secretary of state]; we're asking he look at it and consider the issues on all the planning issues."

English Heritage believes it is possible to find a compromise that does not mean the city will lose its world heritage status.

The world heritage status inscription describes Liverpool as the "supreme example of a commercial port at the time of Britain's greatest global influence". English Heritage says the dockland landscape bears testimony to this international significance.

Owen-John said it was disappointing that after four years of detailed discussion, "we still have a scheme that harms heritage".

The delegation warned the skyscraper proposal would result in a "serious loss of historic authenticity". The inspectors praised the more or less symmetrical profile of the city's waterfront with the Three Graces – the Port of Liverpool and the Liver and Cunard buildings – at centre stage and historical docklands to the north complementing those to the south.

The Graces were "at the heart of the shipping and harbour operations during the height of [Liverpool's] glory, surrounded by dockyards and port structure", it said.

The £5.5bn Peel Holdings scheme has been a source of controversy and English Heritage has been in talks with the developer for four years attempting to find a compromise.

But Unesco did not spell out what would happen to the city's world heritage status if no changes were made to the project. It had been feared the report would recommend removing the status if the scheme was given planning permission, but it did not go that far.

Peel Holdings has previously agreed to scale down the height of the Shanghai Tower to address heritage concerns.

Liverpool city council's planning committee will consider the proposal on 6 March.

Joe Anderson, the leader of Liverpool city council, has previously indicated that he welcomed the Unesco report's findings and was pressing for a compromise that would enable Liverpool Waters to go ahead.

He regards the plans as vital for the future of what is one of the poorest areas of the country.

• This article was amended on 24 February 2012. The original described Peel Holdings as current owner of Manchester's Trafford Centre. Peel Holdings points out that Capital Shopping Centres now owns The Trafford Centre, after buying it from Peel in January 2011 for £1.6bn